PROJECT SUMMARY The genomes of microbes and their hosts are intertwined through time. Pathogenic microbes evolve mechanisms to manipulate host cell functions and hosts evolve mechanisms defending from infections. Buried in this evolutionary history of host-microbial conflict are genetically encoded innovations conferring pivotal advantages. Sometimes the discovery of these functions presents an opportunity to harness the process as a research tool. Antibodies, restriction endonucleases, and CRISPR/Cas systems are examples of natural immune processes repurposed to revolutionize modern biology. A central premise of this proposal is to take a similar view of host-microbe conflict as a crucible for biological innovation. Our approach guides rigorous multidisciplinary studies using complementary computational and experimental analysis to investigate diverse host and microbe processes. Our work is revealing a new class of broadly acting antiviral functions. By considering the evolutionary implications of enveloped viruses exploiting the endosomal sorting complex required for transport (ESCRT) pathway, we discovered a new host immune function, encoded by retroCHMP3, that can block the release of maturing virus particles from infected cells. In addition to characterizing the evolutionary process leading to this specific biological innovation, we will develop new computational pipelines to discover related antimicrobial functions in genomes of diverse mammals. The work is also revealing a primary role for retrotransposons and other selfish genetic elements in creating and regulating genes involved in host-virus conflicts. New discoveries related to the activity of selfish genes also applies to our work on DNA virus evolution. Using vaccinia virus as a model system for large DNA virus evolution, we are pursuing several experimental schemes revealing mechanisms of virus adaptation. One example tackles the question of how viruses acquire host genes through horizontal transfer, a mechanism of adaptation common in diverse virus classes. Discovering a primary role for retrotransposons in mobilizing host transcripts to virus genomes connects classic work on phage transduction in bacteria with eukaryotic systems and opens a range of new questions related to virus control of genetic exchange among diverse species. Finally, we will extend our studies to host systems outside dedicated immune defenses, including a project studying intriguing signals of rapid evolution in proteins regulating water balance in the intestine. These genetic conflicts involve enteric pathogens causing diarrhea and guide new studies aimed at repurposing host peptide variants as novel antibiotic strategies.